admin/gitlab-ci/gromacs.gitlab-ci.yml

   1 # Build, test, and install variously configured GROMACS installations.
   2
   3 # Initial build that always needs to pass before follow-up stages run
   4 simple-build:
   5   extends:
   6     - .variables:default
   7     - .use-ccache
   8     - .use-clang:base
   9     - .rules:basic-push
  10   stage: pre-build
  11   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
  12   tags: []
  13   variables:
  14     KUBERNETES_CPU_LIMIT: 8
  15     KUBERNETES_CPU_REQUEST: 4
  16     KUBERNETES_MEMORY_LIMIT: 8Gi
  17     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
  18     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  19     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  20     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  21     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  22     CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
  23     COMPILER_MAJOR_VERSION: 9
  24     BUILD_DIR: simple-build
  25   script:
  26     - echo $CMAKE_COMPILER_SCRIPT
  27     - echo $CMAKE_EXTRA_OPTIONS
  28     - echo $CMAKE_SIMD_OPTIONS
  29     - echo $CMAKE_GPU_OPTIONS
  30     - echo $CMAKE_MPI_OPTIONS
  31     - echo $CMAKE_PRECISION_OPTIONS
  32     - echo $CMAKE_BUILD_TYPE_OPTIONS
  33     - echo $CMAKE_GMXAPI_OPTIONS
  34     - if [[ -d $BUILD_DIR ]] ; then
  35       echo "Cleaning up build directory" ;
  36       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
  37       else
  38       echo "Preparing new build directory" ;
  39       mkdir $BUILD_DIR ;
  40       fi
  41     - cd $BUILD_DIR
  42     - cmake ..
  43       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
  44       $CMAKE_COMPILER_SCRIPT
  45       $CMAKE_EXTRA_OPTIONS
  46       $CMAKE_SIMD_OPTIONS
  47       $CMAKE_MPI_OPTIONS
  48       $CMAKE_PRECISION_OPTIONS
  49       $CMAKE_BUILD_TYPE_OPTIONS
  50       $CMAKE_GPU_OPTIONS
  51       $CMAKE_GMXAPI_OPTIONS
  52       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
  53       2>&1 | tee cmakeLog.log
  54     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
  55     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
  56     - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
  57     - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
  58     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
  59       | grep -v "CMake" | tee buildErrors.log || true
  60     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
  61     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
  62     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
  63     - ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
  64     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
  65       ctestLog.log | tee ctestErrors.log
  66     - xsltproc scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml
  67     - if [ -s ctestErrors.log ] ; then
  68       echo "Error during running ctest";
  69       exit 1;
  70       fi
  71     - cd ..
  72   artifacts:
  73     reports:
  74       junit: $BUILD_DIR/JUnitTestResults.xml
  75     paths:
  76       - $BUILD_DIR/*log
  77     when: always
  78     expire_in: 1 week
  79
  80 # Jobs running in first pre-build stage
  81
  82 .gromacs:base:configure:
  83   extends:
  84     - .variables:default
  85   stage: configure-build
  86   cache: {}
  87   variables:
  88     KUBERNETES_CPU_LIMIT: 1
  89     KUBERNETES_CPU_REQUEST: 1
  90     KUBERNETES_MEMORY_LIMIT: 2Gi
  91     CMAKE_COMPILER_SCRIPT: ""
  92     CMAKE_EXTRA_OPTIONS: ""
  93     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
  94     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  95     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  96     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  97     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  98   script:
  99     - echo $CMAKE_COMPILER_SCRIPT
 100     - echo $CMAKE_EXTRA_OPTIONS
 101     - echo $CMAKE_SIMD_OPTIONS
 102     - echo $CMAKE_GPU_OPTIONS
 103     - echo $CMAKE_MPI_OPTIONS
 104     - echo $CMAKE_PRECISION_OPTIONS
 105     - echo $CMAKE_BUILD_TYPE_OPTIONS
 106     - echo $CMAKE_GMXAPI_OPTIONS
 107     - if [[ -d $BUILD_DIR ]] ; then
 108       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
 109       else
 110       echo "Preparing new build directory" ;
 111       mkdir $BUILD_DIR ;
 112       fi
 113     - cd $BUILD_DIR
 114     - cmake ..
 115       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 116       $CMAKE_COMPILER_SCRIPT
 117       $CMAKE_EXTRA_OPTIONS
 118       $CMAKE_SIMD_OPTIONS
 119       $CMAKE_MPI_OPTIONS
 120       $CMAKE_PRECISION_OPTIONS
 121       $CMAKE_BUILD_TYPE_OPTIONS
 122       $CMAKE_GPU_OPTIONS
 123       $CMAKE_GMXAPI_OPTIONS
 124       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
 125       2>&1 | tee cmakeLog.log
 126     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 127     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 128     - cd ..
 129   artifacts:
 130     when: always
 131     paths:
 132       - $BUILD_DIR
 133
 134 .gromacs:base:release:configure:
 135   extends:
 136     - .variables:default
 137   stage: release-configure
 138   cache: {}
 139   variables:
 140     KUBERNETES_CPU_LIMIT: 1
 141     KUBERNETES_CPU_REQUEST: 1
 142     KUBERNETES_MEMORY_LIMIT: 2Gi
 143     CMAKE_COMPILER_SCRIPT: ""
 144     CMAKE_EXTRA_OPTIONS: ""
 145     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
 146     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
 147     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
 148     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 149     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
 150     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
 151     RELEASE_BUILD_DIR: release-builds
 152     RELEASE_SOURCE: release-source-from-tarball
 153     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
 154   script:
 155     - VERSION=`cat version.json |
 156       python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
 157     - if [[ $GROMACS_RELEASE != "true" ]] ; then
 158       VERSION=$VERSION-dev ;
 159       fi
 160     - SOURCENAME=gromacs-$VERSION
 161     - SOURCETARBALL=$SOURCENAME.tar.gz
 162     - REGTESTNAME=regressiontests-$VERSION
 163     - REGTESTTARBALL=$REGTESTNAME.tar.gz
 164     - echo "$SOURCETARBALL"
 165     - echo "$REGTESTTARBALL"
 166     - RELEASE_TARBALLS=release-tarballs
 167     - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
 168     - mv $SOURCETARBALL $RELEASE_TARBALLS
 169     - mv $REGTESTTARBALL $RELEASE_TARBALLS
 170     - cd $RELEASE_TARBALLS
 171     # We rename the source and regressiontest directories
 172     # to have names for them that don't change for different versions.
 173     - tar -xf $SOURCETARBALL
 174     - mv $SOURCENAME ../$RELEASE_SOURCE
 175     - tar -xf $REGTESTTARBALL
 176     - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
 177     - rm $SOURCETARBALL $REGTESTTARBALL
 178     - cd ..
 179     - echo $CMAKE_COMPILER_SCRIPT
 180     - echo $CMAKE_EXTRA_OPTIONS
 181     - echo $CMAKE_SIMD_OPTIONS
 182     - echo $CMAKE_GPU_OPTIONS
 183     - echo $CMAKE_MPI_OPTIONS
 184     - echo $CMAKE_PRECISION_OPTIONS
 185     - echo $CMAKE_BUILD_TYPE_OPTIONS
 186     - echo $CMAKE_GMXAPI_OPTIONS
 187     - if [[ -d $RELEASE_BUILD_DIR ]] ; then
 188       echo "Cleaning up build directory" ;
 189       rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
 190       else
 191       echo "Preparing new build directory" ;
 192       mkdir $RELEASE_BUILD_DIR ;
 193       fi
 194     - cd $RELEASE_BUILD_DIR
 195     - cmake ../$RELEASE_SOURCE/
 196       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 197       $CMAKE_COMPILER_SCRIPT
 198       $CMAKE_EXTRA_OPTIONS
 199       $CMAKE_SIMD_OPTIONS
 200       $CMAKE_MPI_OPTIONS
 201       $CMAKE_PRECISION_OPTIONS
 202       $CMAKE_BUILD_TYPE_OPTIONS
 203       $CMAKE_GPU_OPTIONS
 204       $CMAKE_GMXAPI_OPTIONS
 205       $CMAKE_REGRESSIONTEST_OPTIONS
 206       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
 207       2>&1 | tee cmakeLog.log
 208     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 209     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 210     - cd ..
 211   artifacts:
 212     when: always
 213     paths:
 214       - $RELEASE_BUILD_DIR
 215       - $RELEASE_REGRESSIONTESTS
 216       - $RELEASE_SOURCE
 217
 218 # Templates for configuration stage
 219
 220 gromacs:gcc-7:configure:
 221   extends:
 222     - .gromacs:base:configure
 223     - .use-gcc:base
 224     - .use-opencl
 225     - .rules:merge-requests
 226   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 227   variables:
 228     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 229     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 230     COMPILER_MAJOR_VERSION: 7
 231
 232 gromacs:gcc-8:configure:
 233   extends:
 234     - .gromacs:base:configure
 235     - .use-gcc:base
 236     - .use-cuda
 237     - .rules:merge-requests
 238   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 239   variables:
 240     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 241     COMPILER_MAJOR_VERSION: 8
 242
 243 gromacs:clang-TSAN:configure:
 244   extends:
 245     - .gromacs:base:configure
 246     - .use-clang:base
 247     - .rules:merge-requests
 248   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 249   variables:
 250     COMPILER_MAJOR_VERSION: 8
 251     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
 252
 253 gromacs:clang-8:configure:
 254   extends:
 255     - .gromacs:base:configure
 256     - .use-clang:base
 257     - .rules:merge-requests
 258   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 259   variables:
 260     COMPILER_MAJOR_VERSION: 8
 261
 262 gromacs:clang-9:configure:
 263   extends:
 264    - .gromacs:base:configure
 265    - .use-clang:base
 266    - .use-mpi
 267    - .rules:merge-requests
 268   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 269   variables:
 270     COMPILER_MAJOR_VERSION: 9
 271     CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
 272
 273 gromacs:clang-static-analyzer:configure:
 274   extends:
 275     - .gromacs:base:configure
 276     - .use-clang:base
 277     - .rules:merge-requests
 278   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 279   variables:
 280      CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
 281      CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
 282      CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
 283
 284 gromacs:clang-ASAN:configure:
 285   extends:
 286     - .gromacs:base:configure
 287     - .use-clang:base
 288     - .rules:merge-requests
 289   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 290   variables:
 291     COMPILER_MAJOR_VERSION: 8
 292     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
 293
 294 gromacs:gcc-8:release:configure:
 295   extends:
 296     - .gromacs:base:release:configure
 297     - .use-gcc:base
 298     - .use-mpi
 299     - .use-cuda
 300     - .rules:nightly-only-for-release
 301   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 302   variables:
 303     COMPILER_MAJOR_VERSION: 8
 304     RELEASE_BUILD_DIR: release-builds-gcc
 305     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 306     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebug"
 307     CMAKE_REGRESSIONTEST_OPTIONS: ""
 308   dependencies:
 309     - archive:package
 310     - regressiontests:package
 311     - prepare-release-version
 312
 313 gromacs:gcc-7:release:configure:
 314   extends:
 315     - .gromacs:base:release:configure
 316     - .use-gcc:base
 317     - .rules:nightly-only-for-release
 318   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 319   variables:
 320     COMPILER_MAJOR_VERSION: 7
 321     RELEASE_BUILD_DIR: release-builds-gcc
 322     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 323   dependencies:
 324     - archive:package
 325     - regressiontests:package
 326     - prepare-release-version
 327
 328 gromacs:clang-9:release:configure:
 329   extends:
 330     - .gromacs:base:release:configure
 331     - .use-clang:base
 332     - .use-mpi
 333     - .rules:nightly-only-for-release
 334   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 335   variables:
 336     COMPILER_MAJOR_VERSION: 9
 337     RELEASE_BUILD_DIR: release-builds-clang
 338     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 339     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 340   dependencies:
 341     - archive:package
 342     - regressiontests:package
 343     - prepare-release-version
 344
 345 gromacs:clang-8:release:configure:
 346   extends:
 347     - .gromacs:base:release:configure
 348     - .use-clang:base
 349     - .use-cuda
 350     - .rules:nightly-only-for-release
 351   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 352   variables:
 353     COMPILER_MAJOR_VERSION: 8
 354     RELEASE_BUILD_DIR: release-builds-clang
 355     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebug"
 356
 357 # Jobs running during build stage
 358
 359 .gromacs:base:build:
 360   stage: build
 361   script:
 362     - cd $BUILD_DIR
 363     - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 364     - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
 365     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 366       | grep -v "CMake" | tee buildErrors.log || true
 367     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 368     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 369     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 370     - cd ..
 371   artifacts:
 372     when: always
 373     paths:
 374       - $BUILD_DIR
 375       - $INSTALL_DIR/
 376
 377 .gromacs:static-analyzer-build:
 378   stage: build
 379   script:
 380     - cd $BUILD_DIR
 381     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 382     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 383       | grep -v "CMake" | tee buildErrors.log || true
 384     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 385     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 386     - cd ..
 387   artifacts:
 388     when: always
 389     paths:
 390       - $BUILD_DIR/scan_html
 391
 392 gromacs:gcc-7:build:
 393   extends:
 394     - .variables:default
 395     - .gromacs:base:build
 396     - .before_script:default
 397     - .use-ccache
 398     - .rules:merge-requests
 399   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 400   needs:
 401     - job: gromacs:gcc-7:configure
 402       artifacts: true
 403
 404 gromacs:gcc-8:build:
 405   extends:
 406     - .variables:default
 407     - .gromacs:base:build
 408     - .before_script:default
 409     - .use-ccache
 410     - .rules:merge-requests
 411   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 412   needs:
 413     - job: gromacs:gcc-8:configure
 414
 415 gromacs:clang-TSAN:build:
 416   extends:
 417     - .variables:default
 418     - .gromacs:base:build
 419     - .use-clang:base
 420     - .use-ccache
 421     - .rules:merge-requests
 422   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 423   needs:
 424     - job: gromacs:clang-TSAN:configure
 425
 426 gromacs:clang-ASAN:build:
 427   extends:
 428     - .variables:default
 429     - .gromacs:base:build
 430     - .use-clang:base
 431     - .use-ccache
 432     - .rules:merge-requests
 433   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 434   needs:
 435     - job: gromacs:clang-ASAN:configure
 436
 437 gromacs:clang-static-analyzer:build:
 438   extends:
 439     - .variables:default
 440     - .gromacs:static-analyzer-build
 441     - .use-clang:base
 442     - .use-ccache
 443     - .rules:merge-requests
 444   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 445   needs:
 446     - job: gromacs:clang-static-analyzer:configure
 447
 448 gromacs:clang-8:build:
 449   extends:
 450     - .variables:default
 451     - .gromacs:base:build
 452     - .before_script:default
 453     - .use-ccache
 454     - .rules:merge-requests
 455   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 456   needs:
 457     - job: gromacs:clang-8:configure
 458
 459 gromacs:clang-9:build:
 460   extends:
 461     - .variables:default
 462     - .gromacs:base:build
 463     - .before_script:default
 464     - .use-ccache
 465     - .rules:merge-requests
 466   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 467   needs:
 468     - job: gromacs:clang-9:configure
 469
 470 gromacs:gcc-8:release:build:
 471   extends:
 472     - .variables:default
 473     - .gromacs:base:build
 474     - .before_script:default
 475     - .use-ccache
 476     - .rules:nightly-only-for-release
 477   stage: release-build
 478   variables:
 479     BUILD_DIR: release-builds-gcc
 480   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 481   needs:
 482     - job: gromacs:gcc-8:release:configure
 483
 484 gromacs:gcc-7:release:build:
 485   extends:
 486     - .variables:default
 487     - .gromacs:base:build
 488     - .before_script:default
 489     - .use-ccache
 490     - .rules:nightly-only-for-release
 491   stage: release-build
 492   variables:
 493     BUILD_DIR: release-builds-gcc
 494   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 495   needs:
 496     - job: gromacs:gcc-7:release:configure
 497
 498 gromacs:clang-9:release:build:
 499   extends:
 500     - .variables:default
 501     - .gromacs:base:build
 502     - .before_script:default
 503     - .use-ccache
 504     - .rules:nightly-only-for-release
 505   stage: release-build
 506   variables:
 507     BUILD_DIR: release-builds-clang
 508   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 509   needs:
 510     - job: gromacs:clang-9:release:configure
 511
 512 gromacs:clang-8:release:build:
 513   extends:
 514     - .variables:default
 515     - .gromacs:base:build
 516     - .before_script:default
 517     - .use-ccache
 518     - .rules:nightly-only-for-release
 519   stage: release-build
 520   variables:
 521     BUILD_DIR: release-builds-clang
 522   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 523   needs:
 524     - job: gromacs:clang-8:release:configure
 525
 526 # Jobs running during test stage
 527
 528 .gromacs:base:test:
 529   extends:
 530     - .variables:default
 531   stage: test
 532   cache: {}
 533   retry:
 534     max: 1
 535   variables:
 536     CTEST_RUN_MODE: "ExperimentalTest"
 537   script:
 538     - cd $BUILD_DIR
 539     # Needed to run MPI enabled code in the docker images, until we set up different users
 540     - export OMPI_ALLOW_RUN_AS_ROOT=1
 541     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 542     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 543     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 544       ctestLog.log | tee ctestErrors.log
 545     - xsltproc scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 546     - if [ -s ctestErrors.log ] ; then
 547       echo "Error during running ctest";
 548       exit 1;
 549       fi
 550     - cd ..
 551   artifacts:
 552     reports:
 553       junit: $BUILD_DIR/JUnitTestResults.xml
 554     paths:
 555       - $BUILD_DIR/Testing
 556       - $BUILD_DIR/tests
 557     when: always
 558     expire_in: 1 week
 559
 560 .gromacs:base:regressiontest:
 561   extends:
 562     - .variables:default
 563   variables:
 564     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 565     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 566     REGRESSIONTEST_PME_RANK_NUMBER: 1
 567     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 568     REGRESSIONTEST_DOUBLE: ""
 569     REGRESSIONTEST_PARALLEL: "-nt"
 570   stage: test
 571   cache: {}
 572   retry:
 573     max: 1
 574   script:
 575     # This should go away once we are able to run ASAN on mdrun
 576     - export ASAN_OPTIONS="detect_leaks=0"
 577     # Needed to run MPI enabled code in the docker images, until we set up different users
 578     - export OMPI_ALLOW_RUN_AS_ROOT=1
 579     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 580     - tar xzf gmx-regressiontests.tar.gz
 581     - source $INSTALL_DIR/bin/GMXRC
 582     - cd regressiontests
 583     - perl gmxtest.pl $REGRESSIONTEST_PARALLEL $REGRESSIONTEST_TOTAL_RANK_NUMBER -ntomp $REGRESSIONTEST_OMP_RANK_NUMBER -npme $REGRESSIONTEST_PME_RANK_NUMBER $REGRESSIONTEST_DOUBLE $REGRESSIONTEST_MPI_RUN_COMMAND -xml all
 584   artifacts:
 585     paths:
 586       - regressiontests/gmxtest.xml
 587     when: always
 588     expire_in: 1 week
 589
 590 gromacs:gcc-7:test:
 591   extends:
 592     - .gromacs:base:test
 593     - .rules:merge-requests
 594   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 595   variables:
 596     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 597     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 598   needs:
 599     - job: gromacs:gcc-7:build
 600
 601 gromacs:gcc-8:test:
 602   extends:
 603     - .gromacs:base:test
 604     - .rules:merge-requests
 605   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 606   variables:
 607     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 608     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 609   needs:
 610     - job: gromacs:gcc-8:build
 611
 612 gromacs:clang-8:test:
 613   extends:
 614     - .gromacs:base:test
 615     - .rules:merge-requests
 616   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 617   needs:
 618     - job: gromacs:clang-8:build
 619
 620 gromacs:clang-TSAN:test:
 621   extends:
 622     - .gromacs:base:test
 623     - .rules:merge-requests
 624   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 625   needs:
 626     - job: gromacs:clang-TSAN:build
 627
 628 gromacs:clang-ASAN:test:
 629   extends:
 630     - .gromacs:base:test
 631     - .use-clang:base
 632     - .rules:merge-requests
 633   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 634   variables:
 635     CTEST_RUN_MODE: "ExperimentalMemCheck"
 636   needs:
 637     - job: gromacs:clang-ASAN:build
 638
 639 gromacs:clang-9:test:
 640   extends:
 641     - .gromacs:base:test
 642     - .rules:merge-requests
 643   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 644   needs:
 645     - job: gromacs:clang-9:build
 646
 647 gromacs:gcc-7:regressiontest:
 648   extends:
 649     - .gromacs:base:regressiontest
 650     - .rules:merge-requests
 651   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 652   variables:
 653     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 654     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 655     REGRESSIONTEST_PME_RANK_NUMBER: 0
 656     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 657     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 658   needs:
 659     - job: gromacs:gcc-7:build
 660     - job: regressiontests:prepare
 661
 662 gromacs:gcc-8:regressiontest:
 663   extends:
 664     - .gromacs:base:regressiontest
 665     - .rules:merge-requests
 666   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 667   variables:
 668     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 669     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 670     REGRESSIONTEST_PME_RANK_NUMBER: 0
 671     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 672     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 673   needs:
 674     - job: gromacs:gcc-8:build
 675     - job: regressiontests:prepare
 676
 677 gromacs:clang-8:regressiontest:
 678   extends:
 679     - .gromacs:base:regressiontest
 680     - .rules:merge-requests
 681   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 682   needs:
 683     - job: gromacs:clang-8:build
 684     - job: regressiontests:prepare
 685
 686 gromacs:clang-TSAN:regressiontest:
 687   extends:
 688     - .gromacs:base:regressiontest
 689     - .rules:merge-requests
 690   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 691   needs:
 692     - job: gromacs:clang-TSAN:build
 693     - job: regressiontests:prepare
 694
 695 gromacs:clang-ASAN:regressiontest:
 696   extends:
 697     - .gromacs:base:regressiontest
 698     - .use-clang:base
 699     - .rules:merge-requests
 700   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 701   needs:
 702     - job: gromacs:clang-ASAN:build
 703     - job: regressiontests:prepare
 704
 705 gromacs:clang-9:regressiontest:
 706   extends:
 707     - .gromacs:base:regressiontest
 708     - .rules:merge-requests
 709   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 710   variables:
 711     REGRESSIONTEST_DOUBLE: "-double"
 712     REGRESSIONTEST_PARALLEL: "-np"
 713   needs:
 714     - job: gromacs:clang-9:build
 715     - job: regressiontests:prepare
 716
 717 gromacs:gcc-8:release:test:
 718   extends:
 719     - .gromacs:base:test
 720     - .rules:nightly-only-for-release
 721   stage: release-tests
 722   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 723   variables:
 724     BUILD_DIR: release-builds-gcc
 725   needs:
 726     - job: gromacs:gcc-8:release:configure
 727     - job: gromacs:gcc-8:release:build
 728
 729 gromacs:gcc-7:release:test:
 730   extends:
 731     - .gromacs:base:test
 732     - .rules:nightly-only-for-release
 733   stage: release-tests
 734   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 735   variables:
 736     BUILD_DIR: release-builds-gcc
 737   needs:
 738     - job: gromacs:gcc-7:release:configure
 739     - job: gromacs:gcc-7:release:build
 740
 741 gromacs:clang-9:release:test:
 742   extends:
 743     - .gromacs:base:test
 744     - .rules:nightly-only-for-release
 745   stage: release-tests
 746   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 747   variables:
 748     BUILD_DIR: release-builds-clang
 749   needs:
 750     - job: gromacs:clang-9:release:configure
 751     - job: gromacs:clang-9:release:build
 752
 753 gromacs:clang-8:release:test:
 754   extends:
 755     - .gromacs:base:test
 756     - .rules:nightly-only-for-release
 757   stage: release-tests
 758   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 759   variables:
 760     BUILD_DIR: release-builds-clang
 761   needs:
 762     - job: gromacs:clang-8:release:configure
 763     - job: gromacs:clang-8:release:build
 764
 765 gromacs:gcc-7:release:regressiontest:
 766   extends:
 767     - .gromacs:base:regressiontest
 768     - .rules:nightly-only-for-release
 769   stage: release-tests
 770   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 771   variables:
 772     BUILD_DIR: release-builds-gcc
 773   needs:
 774     - job: gromacs:gcc-7:release:build
 775     - job: regressiontests:package
 776
 777 gromacs:clang-9:release:regressiontest:
 778   extends:
 779     - .gromacs:base:regressiontest
 780     - .rules:nightly-only-for-release
 781   stage: release-tests
 782   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 783   variables:
 784     BUILD_DIR: release-builds-clang
 785     REGRESSIONTEST_DOUBLE: "-double"
 786     REGRESSIONTEST_PARALLEL: "-np"
 787   needs:
 788     - job: gromacs:clang-9:release:build
 789     - job: regressiontests:package
 790
 791 gromacs:clang-8:release:regressiontest:
 792   extends:
 793     - .gromacs:base:regressiontest
 794     - .rules:nightly-only-for-release
 795   stage: release-tests
 796   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 797   variables:
 798     BUILD_DIR: release-builds-clang
 799     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 800     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 801     REGRESSIONTEST_PME_RANK_NUMBER: 0
 802     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 803     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 804
 805   needs:
 806     - job: gromacs:clang-8:release:build
 807     - job: regressiontests:package
 808